Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018962.1 Corchorus olitorius cultivar O-4 contig18995, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 14681
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:7484 original size:2 final size:2
Alignment explanation
Indices: 7477--7505 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7467 TCACTCAAAA
7477 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7506 CTAGTTTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7594 original size:22 final size:22
Alignment explanation
Indices: 7568--7694 Score: 67
Period size: 22 Copynumber: 5.7 Consensus size: 22
7558 AATATTCTTG
7568 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCACACTA
* ** * **
7590 TGAAATTTTTATAATTACCCCG
1 TGAAATTTTGATAACCACACTA
* *** * *
7612 TGAAATTGTGATAAATTCCCAA
1 TGAAATTTTGATAACCACACTA
**
7634 TGAAATACTGATAACCTA-ACTA
1 TGAAATTTTGATAACC-ACACTA
* ***
7656 TGAAATTTTAATAAACCTTTCTA
1 TGAAATTTTGAT-AACCACACTA
7679 TGAAATTTTGATAACC
1 TGAAATTTTGATAACC
7695 TCCATATGAT
Statistics
Matches: 77, Mismatches: 25, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
22 59 0.77
23 18 0.23
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.35
Consensus pattern (22 bp):
TGAAATTTTGATAACCACACTA
Found at i:8524 original size:17 final size:18
Alignment explanation
Indices: 8502--8535 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
8492 CGAGGTAAGG
*
8502 CGGTTT-GGTGGTTTAAT
1 CGGTTTAGGCGGTTTAAT
8519 CGGTTTAGGCGGTTTAA
1 CGGTTTAGGCGGTTTAA
8536 CCGTCACCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.09, G:0.35, T:0.41
Consensus pattern (18 bp):
CGGTTTAGGCGGTTTAAT
Found at i:8686 original size:11 final size:11
Alignment explanation
Indices: 8670--8732 Score: 67
Period size: 11 Copynumber: 5.9 Consensus size: 11
8660 ATTATTTATG
8670 ATATATATAAA
1 ATATATATAAA
*
8681 ATATATGT-AA
1 ATATATATAAA
8691 A-ATATATAAA
1 ATATATATAAA
* * **
8701 TTATATTTATG
1 ATATATATAAA
8712 ATATATATAAA
1 ATATATATAAA
8723 ATATATATAA
1 ATATATATAA
8733 TAAACTATTT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
9 5 0.12
10 5 0.12
11 30 0.75
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (11 bp):
ATATATATAAA
Found at i:8697 original size:20 final size:21
Alignment explanation
Indices: 8672--8728 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
8662 TATTTATGAT
8672 ATATATAAAATATATGTA-AA
1 ATATATAAAATATATGTAGAA
* * *
8692 ATATATAAATTATATTTATGAT
1 ATATATAAAATATATGTA-GAA
8714 ATATATAAAATATAT
1 ATATATAAAATATAT
8729 ATAATAAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 16 0.52
22 15 0.48
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (21 bp):
ATATATAAAATATATGTAGAA
Found at i:9310 original size:58 final size:58
Alignment explanation
Indices: 9248--9362 Score: 230
Period size: 58 Copynumber: 2.0 Consensus size: 58
9238 GGCATAGAGA
9248 TTTATTTGAATTGAATTGTAATGAGATTTCTTGGATTTGTTTGTTGGGAAATCATGTG
1 TTTATTTGAATTGAATTGTAATGAGATTTCTTGGATTTGTTTGTTGGGAAATCATGTG
9306 TTTATTTGAATTGAATTGTAATGAGATTTCTTGGATTTGTTTGTTGGGAAATCATGT
1 TTTATTTGAATTGAATTGTAATGAGATTTCTTGGATTTGTTTGTTGGGAAATCATGT
9363 AGCAGTGTAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.24, C:0.03, G:0.23, T:0.49
Consensus pattern (58 bp):
TTTATTTGAATTGAATTGTAATGAGATTTCTTGGATTTGTTTGTTGGGAAATCATGTG
Found at i:11241 original size:161 final size:161
Alignment explanation
Indices: 11059--11381 Score: 610
Period size: 161 Copynumber: 2.0 Consensus size: 161
11049 ATCTATGGTG
* *
11059 CAACTAGTCAGTCCAACACACACTTGAATTAATCAAAGGTTGACTTCACATGGGATATTAACAGA
1 CAACAAGTCAGTACAACACACACTTGAATTAATCAAAGGTTGACTTCACATGGGATATTAACAGA
*
11124 GATTTATTAGTAATAAGCTAATTTCCCGGCAACTTCTTGGTACAAATAAAAAATTTGGAAAGAGT
66 GATTTATTAGTAATAAGCTAATTTCCCGGCAACTTCTTGGTACAAATAAAAAAATTGGAAAGAGT
11189 GAGGACAACGTTTTTAGGTGAAAGATGAAAA
131 GAGGACAACGTTTTTAGGTGAAAGATGAAAA
11220 CAACAAGTCAGTACAACACACACTTGAATTAATCAAAGGTTGACTTCACATGGGATATTAACAGA
1 CAACAAGTCAGTACAACACACACTTGAATTAATCAAAGGTTGACTTCACATGGGATATTAACAGA
*
11285 GATTTATTAGTAATAAGCTACTTTCCCGGCAACTTCTTGGTACAAATAAAAAAATTGGAAAGAGT
66 GATTTATTAGTAATAAGCTAATTTCCCGGCAACTTCTTGGTACAAATAAAAAAATTGGAAAGAGT
11350 GAGGACAACGTTTTTAGGTGAAAGATGAAAA
131 GAGGACAACGTTTTTAGGTGAAAGATGAAAA
11381 C
1 C
11382 CCATTTTCTG
Statistics
Matches: 158, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
161 158 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (161 bp):
CAACAAGTCAGTACAACACACACTTGAATTAATCAAAGGTTGACTTCACATGGGATATTAACAGA
GATTTATTAGTAATAAGCTAATTTCCCGGCAACTTCTTGGTACAAATAAAAAAATTGGAAAGAGT
GAGGACAACGTTTTTAGGTGAAAGATGAAAA
Found at i:12112 original size:26 final size:27
Alignment explanation
Indices: 12068--12122 Score: 94
Period size: 26 Copynumber: 2.1 Consensus size: 27
12058 TATTTTAAAG
*
12068 CAGAAGAAAAAAATTTCAGAACAAAAC
1 CAGAAGAAAAAAATCTCAGAACAAAAC
12095 CAGAAG-AAAAAATCTCAGAACAAAAC
1 CAGAAGAAAAAAATCTCAGAACAAAAC
12121 CA
1 CA
12123 CAACCAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.62, C:0.18, G:0.11, T:0.09
Consensus pattern (27 bp):
CAGAAGAAAAAAATCTCAGAACAAAAC
Found at i:12443 original size:6 final size:6
Alignment explanation
Indices: 12432--12522 Score: 90
Period size: 6 Copynumber: 16.5 Consensus size: 6
12422 TCTATCTATC
* * *
12432 TATCTA TATCTA TATCTA TA---A TATCTA TATGTA TATTTA TATTTA
1 TATCTA TATCTA TATCTA TATCTA TATCTA TATCTA TATCTA TATCTA
*
12477 TATCTA TATTTA TATC-- TATCTA TATC-- TATCTA TATCTA TAT-TA
1 TATCTA TATCTA TATCTA TATCTA TATCTA TATCTA TATCTA TATCTA
12520 TAT
1 TAT
12523 TAAAAAGTAT
Statistics
Matches: 73, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
3 3 0.04
4 8 0.11
5 5 0.07
6 57 0.78
ACGTcount: A:0.34, C:0.11, G:0.01, T:0.54
Consensus pattern (6 bp):
TATCTA
Found at i:14139 original size:783 final size:784
Alignment explanation
Indices: 12634--14204 Score: 3045
Period size: 783 Copynumber: 2.0 Consensus size: 784
12624 AAATGCCATT
12634 GTTTAGACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCT
1 GTTTAGACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCT
12699 TATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAAAAAAATTATATATATTAGAATTTT
66 TATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAAAAAAATTATATATATTAGAATTTT
12764 TAAATATATTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTGGCAAAAAAAAACTAAAAAC
131 TAAATATATTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTGGCAAAAAAAAACTAAAAAC
12829 TCTATTTTTATTTAATTAAATCTAATATCCTTATACCTATTTTATTTTTATCAATTTACTAATTT
196 TCTATTTTTATTTAATTAAATCTAATATCCTTATACCTATTTTATTTTTATCAATTTACTAATTT
*
12894 AATTAAAAAATTTAGATATATTAGAATTTTTAAAATATAATTCTTAAATGACATTGATTAAATTT
261 AATTAAAAAATTTAGATATATTAGAATTTTTAAAATATAATTCTTAAAGGACATTGATTAAATTT
*
12959 TACAGTTCTTAAAGAAATAAACTTTTACAATTATTCTACTAAAAACTCTATTTTTATTTGATTAA
326 TACAATTCTTAAAGAAATAAACTTTTACAATTATTCTACTAAAAACTCTATTTTTATTTGATTAA
*
13024 ATTCAATATATTTATAAGTATTTTAATTTACCATTTTAATTTTAAAAAATTGGAGACTTTTTTTC
391 ATTCAATATATTTATAAATATTTTAATTTACCATTTTAATTTTAAAAAATTGGAGACTTTTTTTC
13089 AATTATAATATAAACTAATTTGAACAAAAAAAATTATAATATAAACTAACAAAAATCTTATTATC
456 AATTATAATATAAACTAATTTGAACAAAAAAAATTATAATATAAACTAACAAAAATCTTATTATC
13154 AAGTTTAAAAGTTAAAATAATTTACCTAATTTAATTTAAAAAAACTTATAAAATTTTAAAAATAA
521 AAGTTTAAAAGTTAAAATAATTTACCTAATTTAATTTAAAAAAACTTATAAAATTTTAAAAATAA
13219 AAAGAAGAGTAACATGCAATTATTTCATTTGACTTATAAAGTTAGAGGAGTGGGCGGGTTGGACG
586 AAAGAAGAGTAACATGCAATTATTTCATTTGACTTATAAAGTTAGAGGAGTGGGCGGGTTGGACG
*
13284 GCTTTTGGGTTCGGGTCATCTGGGTACAAATCAAATGAGGCAGGTAATTTTCTCGGGACATTAGG
651 GCTTTCGGGTTCGGGTCATCTGGGTACAAATCAAATGAGGCAGGTAATTTTCTCGGGACATTAGG
13349 GTTTCGGCTCATCTAGCTTCAGGTTATTT-GGTCTTGGGTCTGCTGGATCTAGGGTCAGGCGAGT
716 GTTTCGGCTCATCTAGCTTCAGGTTATTTGGGTCTTGGGTCTGCTGGATCTAGGGTCAGGCGAGT
13413 TCGG
781 TCGG
*
13417 GTTTAGACTTTTATAGTTTTACTCAGCTAAAAACTCTATTTTTATTTAATTAAATATAATATCCT
1 GTTTAGACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCT
13482 TATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAAAAAAATTATATATATTAGAATTTT
66 TATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAAAAAAATTATATATATTAGAATTTT
13547 TAAATATATTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTGGCAAAAAAAAACTAAAAAC
131 TAAATATATTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTGGCAAAAAAAAACTAAAAAC
13612 TCTATTTTTATTTAATTAAATCTAATATCCTTATACCTATTTTATTTTTATCAATTTACTAATTT
196 TCTATTTTTATTTAATTAAATCTAATATCCTTATACCTATTTTATTTTTATCAATTTACTAATTT
*
13677 AATTAAAAAATTTAGATATATTAGAATTTTTAAAATATATTTCTTAAAGGACATTGATTAAATTT
261 AATTAAAAAATTTAGATATATTAGAATTTTTAAAATATAATTCTTAAAGGACATTGATTAAATTT
*
13742 TACAATTCTTAAAGAAATTAACTTTTACAATTATTCTACTAAAAACTCTATTTTTATTTGATTAA
326 TACAATTCTTAAAGAAATAAACTTTTACAATTATTCTACTAAAAACTCTATTTTTATTTGATTAA
13807 ATTCAATATATTTATAAATATTTTAATTTACCATTTTAATTTTAAAAAATTGGAGACTTTTTTTC
391 ATTCAATATATTTATAAATATTTTAATTTACCATTTTAATTTTAAAAAATTGGAGACTTTTTTTC
13872 AATTATAATATAAACTAATTTGAACAAAAAAAATTATAATATAAACTAACAAAAATCTTATTATC
456 AATTATAATATAAACTAATTTGAACAAAAAAAATTATAATATAAACTAACAAAAATCTTATTATC
13937 AAGTTTAAAAGTTAAAATAATTTACCTAATTTAATTTAAAAAAACTTATAAAATTTTAAAAATAA
521 AAGTTTAAAAGTTAAAATAATTTACCTAATTTAATTTAAAAAAACTTATAAAATTTTAAAAATAA
14002 AAAGAAGAGTAACATGCAATTATTTCATTTGACTTATAAAGTTAGAGGAGTGGGCGGGTTGGACG
586 AAAGAAGAGTAACATGCAATTATTTCATTTGACTTATAAAGTTAGAGGAGTGGGCGGGTTGGACG
*
14067 GGTTTCGGGTTCGGGTCATCTGGGTACAAATCAAATGAGGCAGGTAATTTTCTCGGGACATTAGG
651 GCTTTCGGGTTCGGGTCATCTGGGTACAAATCAAATGAGGCAGGTAATTTTCTCGGGACATTAGG
* *
14132 GTTTCGGCTCATCTAGCTTCAGGTTATTTGGGTCTTGGGTCTTCTGGATCTAGGGTCAGGCGGGT
716 GTTTCGGCTCATCTAGCTTCAGGTTATTTGGGTCTTGGGTCTGCTGGATCTAGGGTCAGGCGAGT
14197 TCGG
781 TCGG
14201 GTTT
1 GTTT
14205 TGGCCTTAAG
Statistics
Matches: 777, Mismatches: 10, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
783 736 0.95
784 41 0.05
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (784 bp):
GTTTAGACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCT
TATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAAAAAAATTATATATATTAGAATTTT
TAAATATATTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTGGCAAAAAAAAACTAAAAAC
TCTATTTTTATTTAATTAAATCTAATATCCTTATACCTATTTTATTTTTATCAATTTACTAATTT
AATTAAAAAATTTAGATATATTAGAATTTTTAAAATATAATTCTTAAAGGACATTGATTAAATTT
TACAATTCTTAAAGAAATAAACTTTTACAATTATTCTACTAAAAACTCTATTTTTATTTGATTAA
ATTCAATATATTTATAAATATTTTAATTTACCATTTTAATTTTAAAAAATTGGAGACTTTTTTTC
AATTATAATATAAACTAATTTGAACAAAAAAAATTATAATATAAACTAACAAAAATCTTATTATC
AAGTTTAAAAGTTAAAATAATTTACCTAATTTAATTTAAAAAAACTTATAAAATTTTAAAAATAA
AAAGAAGAGTAACATGCAATTATTTCATTTGACTTATAAAGTTAGAGGAGTGGGCGGGTTGGACG
GCTTTCGGGTTCGGGTCATCTGGGTACAAATCAAATGAGGCAGGTAATTTTCTCGGGACATTAGG
GTTTCGGCTCATCTAGCTTCAGGTTATTTGGGTCTTGGGTCTGCTGGATCTAGGGTCAGGCGAGT
TCGG
Done.